Researchers Greatly Improve Evolutionary Tree of Life for Mammals

Posted September 22, 2011

International team, led by Texas A&M and UC Riverside,
provides robust molecular phylogeny for mammalian families.

COLLEGE STATION, TEXAS -An international research team led by
researchers at the Texas A&M University College of Veterinary
Medicine & Biomedical Sciences (CVM) and University of
California, Riverside (UCR) has released for the first time a large
and robust DNA matrix that has representation for 99 percent of
mammalian families, and covers the deepest divergences among all
living mammals.

"Our study, a collaboration led by researchers at Texas A&M
University and the University of California, Riverside together
with members of several international institutions, represents the
culmination of a five year project aimed at using large genetic
datasets to better understand the evolutionary history of mammalian
families and genera," said William Murphy, associate professor in
the Department of Veterinary Integrative Biosciences at the CVM,
who co-led the research project with Mark Springer, professor of
Biology at UCR. "Our findings now clarify how mammals should be
properly classified, and provides us with a better understanding of
the environmental and ecological basis for why mammals diversify,
and a proper comparative and temporal framework for understanding
the genetic changes that have led to their remarkably diversity in
size and form.

Phylogeny is the history of organismal lineages as they change
through time. A vast evolutionary tree, called the Tree of
Life, represents the phylogeny of organisms, the genealogical
relationships of all living things.

As most introductory biology textbooks will show, organisms are
biologically classified according to a hierarchical system
characterized by seven main taxonomic ranks: kingdom, phylum or
division, class, order, family, genus, species. For example,
humans are known taxonomically as Homo sapiens. Their genus
is Homo, the family is Hominidae, the order is Primates and the
class is Mammalia.

"To estimate when different mammal groups split we used a
'relaxed clock' approach which allows rates of DNA to change across
the tree of mammals," said Murphy. "To produce reliable estimates
requires that we have access to a large collection of well
established fossil constraints to estimate rates of changes on
different branches of the tree, and then we can convert the tree of
relationships into a time tree, in which the branches are scaled in
proportion to time. This time tree allows us to examine when
different groups of mammals originated and diversified, and then
associate factors which might have been responsible for these
diversification events."

Study results appear in the September 22 issue of Science
Express.

"Our phylogeny, underpinned by a large number of genes, sets the
stage for us to understand how the different mammalian species are
related to each other," Springer said. "That will help us
understand when these species diverged from each other. It
will allow us to look for taxonomic rates of increase or decrease
over time in different groups in various parts of the world so that
we can understand these diversification rate changes in
relationship to important events in Earth's history - such as the
diversification of flowering plants and changes associated with
climatic events. Researchers routinely make use of phylogenies in
diverse fields such as ecology, physiology, and biogeography, and
the new phylogeny for mammalian families provides a more accurate
framework for these studies.

"When you understand how taxa are related to each other,"
Springer added, "you can start to understand which changes at the
genome level underpin key morphological changes associated with,
say, flight and echolocation in bats or loss of teeth in toothless
mammals. In other words, you can pinpoint key molecular
changes that are associated with key morphological changes.
This would be extremely difficult, if not altogether impossible,
without the kind of robust molecular phylogeny we have
developed."

The research team looked for spikes in the diversification
history of mammals and used an algorithm to determine whether the
rate of diversification was constant over time or whether there
were distinct pulses of rate increases or decreases.

"For example, we observed a distinct pulse of diversification
when most of the mammalian orders began splitting from one another,
near the end of the Cretaceous Terrestrial Revolutions when
flowering plants and insects diversified, and also at a time when
sea levels changed and continental boundaries became reorganized,"
said Murphy.

Murphy and colleagues also detected a second spike in the
diversification history of mammals at the end of the Cretaceous -
65.5 million years ago, when dinosaurs, other large terrestrial
vertebrates, and many marine organisms went extinct, opening up a
vast ecological space.

"We also found evidence that the Cretaceous-Tertiary Mass
extinction, which occurred 65.5 million years ago (Mya) and was
responsible for the demise of the dinosaurs, other large
terrestrial vertebrates and many marine organisms, also promoted
diversification of mammals into their larger and more specialized
modern forms by filling the ecological void left by the organisms
that went extinct," Murphy highlighted.

The research team also reports that their results contradict the
"delayed rise of present-day mammals" hypothesis. According to this
hypothesis, introduced by a team of scientists in a 2007 research
paper, the ancestors of living mammals underwent a pulse of
diversification around 50 million years ago, possibly in response
to the extinction of archaic mammals that went extinct at the end
of the Paleocene (around 56 million years ago). The earlier
extinction event around 65.5 million years ago, which resulted in
the demise of the dinosaurs, had no effect on the diversification
of the ancestors of extant mammals, according to the 2007 research
paper.

"Our results contradict findings of an earlier study published
in 2007 which claimed the rise of modern mammals was somehow
delayed until around 50 Maya, presumably in response to the
extinction of a group of archaic mammals. Our study finds no
evidence for such a delay, and validates a role for the
Cretaceous-Tertiary Mass extinction in the diversification of
modern orders of mammals," Murphy said.

The researchers stress that their time tree is a work in
progress. In the next two years, they expect to construct a
supermatrix, also based on gene sequences, and include the majority
of living mammalian species. The current work incorporates
164 mammalian species.

"This study is the beginning of a larger plan to use large
molecular data sets and sophisticated techniques for dating and
estimating rates of diversification to resolve much larger portions
of the mammalian tree, ultimately including all described species,
as well as those that have gone recently extinct or for which only
museum material may be available," said Murphy. "Only then can we
really begin to understand the role of the environment and events
in earth history in promoting the generation of living
biodiversity. This phylogeny also serves as a framework to
understand the history of the unique changes in the genome that
underlie the vast morphological diversity observed in the more than
5400 living species of mammals."

Murphy and Springer were joined in the study by researchers at
UCR; the San Diego Zoo's Institute for Conservation Research,
Calif.; University College Dublin, Ireland; PUCRS, Brazil;
Eidgenössiche Technische Hochschule Zurich, Switzerland; UC
Berkeley; Pepperdine University, Calif.; American Museum of Natural
History, NY; University of Stellenbosch, South Africa; Chaffey
College, Calif.; LaTrobe University, Australia; and Washington and
Lee University, Virginia.

Jan E. Janecka, research assistant professor in genomics, and
Colleen Fisher, Texas A&M graduate student, in Murphy's
research group performed the bulk of the lab work at Texas A&M.
The UCR researchers include John Gatesy, an associate professor of
biology; Robert Meredith, a postdoctoral researcher and the first
author of the research paper; Angela Burk-Herrick, a former
postdoctoral researcher; and Nadia A. Ayoub, a former postdoctoral
researcher.

Murphy's and Springer's labs were supported by grants from the
National Science Foundation.